What all have you eliminated from your diet - it can take a while for the antibodies/proteins to get out of your system. Also, are you on any Rx meds. The biggest culprit for this problem is dairy. Soy can also contribute, as can wheat. The problem is worse if you also have hidden food allergies (or undiagnosed celiac which is clearly possible given that it's the most commonly undiagnosed disorder) because there are higher amounts of the allergenic proteins circulating in your system and thus in your breastmilk.
Also, more frequent feedings can help reduce the volume he consumes at a feeding and thus improve digestion. You don't mention his feeding schedule at all. Also, keeping him upright after feedings (holding him while he sleeps more upright) will also help alot. Get dad to help out here. Note, that it is also not unheard of for these kids to be born with the reaction to gluten (celiac) if the mother has not been diagnosed, since the fetus will also be exposed to the allergens (same with dairy).
My undiagnosed dairy allergy and celiac were the two things that caused my first child's reflux - the only thing we used were mylicon drops. Also, the problem will improve over time without drugs. The bad thing about those drugs is that inhibit digestion and thus your son may experience a slower weight gain/growth. It's the growth that will help his system mature.
